Hi Ross, Thank you for your reply. I tried it, and it was still not working. Only samtools has this problem, and the other tools works fine. samtools was compiled from source correctly. If I install samtools using "sudo apt-get install samtools", this problem is gone, but this is not a solution for since it does not work across the cluster. Cai --- 12年4月18日，周三, Ross <ross.lazarus@gmail.com> 写道：
发件人: Ross <ross.lazarus@gmail.com> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: "Jennifer Jackson" <jen@bx.psu.edu>, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you are using SGE you probably want to pass the Galaxy user's path to the job using the -V switch in the system wide (or Galaxy user's home directory) sge_request file
eg I have rlazarus@iaas1-int:~$ cat /var/lib/gridengine/default/common/sge_request -cwd -V
Without that switch, the job gets no path. With -V, it inherits the job submitter's full path.
Hi Jen,
Thank you for your quick response. I changed the env.sh file to what you seggested, and
I am pasting more details below:
I submitted a job to convert sam to bam, and the job was running forever without outputing the result. I then checked the log, and it read: Traceback (most recent call last): File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
drm_job_state.job_wrapper.finish( stdout, stderr ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/jobs/__init__.py",
dataset.set_meta( overwrite = False ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/model/__init__.py",
return self.datatype.set_meta( self, **kwd ) File "/mnt/galaxyTools/galaxy-dist/lib/galaxy/datatypes/binary.py",
raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
It means that the samtools is not in the PATH. I tried to set the PATH in a couple of methods according the Galaxy documentation: 1. put the path in the env.sh in the tool directory and symbolink default to the tool directory, e.g. default -> =/mnt/galaxyTools/tools/samtools/0.1.18 2. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in ~/.sge_request 3. put -v PATH=/mnt/galaxyTools/tools/samtools/0.1.18 in /path/sge_request
none of them worked, and I got the above same problem.
Then I checked the job log file in the job_working_directory, and it read: Samtools Version: 0.1.18 (r982:295) SAM file converted to BAM
which shows that sge knows the PATH of samtools. To double check it, I added samtools index to Galaxy, and it worked well. I am very confused why SGE knows the tool path but cannot run the job correctly.
The system I am using is ubuntu on EC2 (the image id is: ami-999d49f0, which is the one used by StarCluster). I checked out the code from galaxy-dist on bitbucket. Other tools such as bwa and bowtie worked well using the same setting method(put env.sh in the tools directory to set the tool path)
Thanks you very much,
Cai --- 12年4月18日，周三, Jennifer Jackson <jen@bx.psu.edu> 写道：
发件人: Jennifer Jackson <jen@bx.psu.edu> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: "zhengqiu cai" <caizhq2005@yahoo.com.cn> 抄送: galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午2:12 Hi Cai,
Please double check that your env.sh file contains
following:
PATH="/mnt/galaxyTools/tools/samtools/0.1.12:$PATH"
export PATH
http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies
Hopefully this helps,
Jen Galaxy team
On 4/16/12 12:43 PM, zhengqiu cai wrote:
Hi All,
I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py",
line 336, in finish_job
drm_job_state.job_wrapper.finish( stdout, stderr ) File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/__init__.py",
line 637, in finish
dataset.set_meta( overwrite = False ) File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/model/__init__.py",
line 875, in set_meta
return self.datatype.set_meta( self, **kwd ) File
"/mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/datatypes/binary.py",
line 179, in set_meta
raise Exception, "Error Setting BAM Metadata: %s" % stderr Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found
I already set the path of samtools Below I pasted how I set the path: ubuntu@master:/mnt/galaxyTools/tools/samtools$ ll total 8 drwxr-xr-x 4 ubuntu ubuntu 65 2012-04-16 19:09 ./ drwxr-xr-x 38 ubuntu ubuntu 4096 2012-04-16 18:41 ../ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-16 19:08 0.1.12/ drwxr-xr-x 2 ubuntu ubuntu 53 2012-04-13 20:23 0.1.7/ lrwxrwxrwx 1 ubuntu ubuntu 38 2012-04-16 19:09 default -> /mnt/galaxyTools/tools/samtools/0.1.12/
ubuntu@master:/mnt/galaxyTools/tools/samtools$ more default/env.sh
PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH
I used the same way to set other programs,
such as bwa and bowtie, and they worked perfectly. Only samtools could not work.
I even used the full path of samtools in the wrapper file sam_to_bam.py, and it was not working neither.
I am wondering if any one met the same
On Tue, Apr 17, 2012 at 4:26 PM, zhengqiu cai <caizhq2005@yahoo.com.cn> wrote: the problem still existed. line 336, in finish_job line 637, in finish line 875, in set_meta line 179, in set_meta the problem, or some
one can give me some hints.
Thank you very much.
Cai
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;